Web Based Genome Browser
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13.0 years ago
Abhi ★ 1.6k

Hi guys

I routinely use IGV for getting a visual feel of our NGS data but now there is a need to have the data we generate be available for public browsing.

I wondering which browser would be nice to use as base. I know Gbrowse and UCSC Genome Browser can be locally installed and run but not sure which is more suited for NGS data.

Ideally we would like to have something which is open source, scalable and adaptive(allows cosmetic changes on data display) and futuristic.

It would be great if you can share your experience.

next-gen sequencing genome • 6.5k views
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Which organism?

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13.0 years ago
Boboppie ▴ 550

Both GBrowse 1.7 and 2.0 support NGS data visualization, see tutorial here and poster here, but several improvements had been made for GBrowse 2 such as updating image via AJAX.JBrowse as the next-generation of GBrowse which is implemented by javascript will certainly bring even faster and smoother experience for users. We have integrated it in our project, and it looks very fancy and portable. It supports viewing NGS data as well, see here, however, as far as I know, it's still under development, and there are bugs yet to fix. You may also consider Dalliance.

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13.0 years ago
Hranjeev ★ 1.5k

Jbrowse is pretty interesting. It looks like an intuitive, responsive and fluid online genome browser to use.

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I like JBrowse : user can add data tracks pretty easily and it is quite responsive (unlike other more popular broswers...)

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13.0 years ago
Mary 11k

Last time this question came up I mentioned WebGBrowse, which could be really handy to set up quick demos I think--but may be lighter than you need. But I forgot to mention Gaggle Genome Browser too.

I did a longer post on that here, Gaggle is a set of things that can work together that might have other appeal too.

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13.0 years ago
Mary 11k

New browser: I'm just starting to look into this, haven't gotten very far--but GenPlay has just been published recently:

Publication: GenPlay, a multi-purpose genome analyzer and browser

GenPlay site: http://genplay.einstein.yu.edu/wiki/index.php/About_GenPlay

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Thanks. I just glanced at the demo. Does one have to download a jnlp each time a new visitor wants to start it. Can it fire up in browser without any download for a new user ?

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I don't know, I just started to look at it myself. You may need to contact them--I don't know if they have a developers mailing list either.

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8.4 years ago

For a light weight solution, try genoverse.

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